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Add initial version of micronutrient extraction template
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id: http://w3id.org/ontogpt/ecosim_methods | ||
name: ecosim_methods | ||
title: EcoSIM Methods Extraction Template | ||
description: >- | ||
EcoSIM Methods Extraction Template | ||
license: https://creativecommons.org/publicdomain/zero/1.0/ | ||
prefixes: | ||
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# | ||
linkml: https://w3id.org/linkml/ | ||
ecosim_simple: http://w3id.org/ontogpt/ecosim_simple | ||
ecosim: http://purl.obolibrary.org/obo/ecosim | ||
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default_prefix: ecosim_methods | ||
default_range: string | ||
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imports: | ||
- linkml:types | ||
- core | ||
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classes: | ||
TermSet: | ||
tree_root: true | ||
is_a: NamedEntity | ||
attributes: | ||
locations: | ||
range: Location | ||
multivalued: true | ||
description: >- | ||
A semicolon-separated list of research locations. | ||
Examples include: Vermont, New York City, | ||
Ethiopia | ||
methods: | ||
range: Method | ||
multivalued: true | ||
description: >- | ||
A semicolon-separated list of methods used in | ||
environmental and earth science research. Examples | ||
include: sampling, spectroscopy | ||
variables: | ||
range: Variable | ||
description: >- | ||
A semicolon-separated list of variables measured in | ||
environmental and earth science research. Examples | ||
include: root shape, biomass, water turbidity | ||
equipments: | ||
range: Equipment | ||
description: >- | ||
A semicolon-separated list of equipment used in | ||
environmental and earth science research. | ||
equipment_to_variable_relationships: | ||
range: EquipmentMeasuresVariable | ||
description: >- | ||
A semicolon separated list of relationships | ||
between specific equipment and variables | ||
they are used to measure as described in the input. | ||
Example: NMR spectrometer was used to measure | ||
chemical content | ||
multivalued: true | ||
inlined: true | ||
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Location: | ||
is_a: NamedEntity | ||
annotations: | ||
prompt: >- | ||
The name of a location used in research. | ||
Method: | ||
is_a: NamedEntity | ||
annotations: | ||
annotators: bioportal:ECOSIM | ||
prompt: >- | ||
The name of a method used in environment and | ||
earth science research. | ||
Variable: | ||
is_a: NamedEntity | ||
annotations: | ||
annotators: bioportal:ECOSIM | ||
prompt: >- | ||
The name of a variable measured in environment and | ||
earth science research. | ||
Equipment: | ||
is_a: NamedEntity | ||
annotations: | ||
prompt: >- | ||
The name of a piece of equipment used in | ||
environment and earth science research. | ||
EquipmentMeasuresVariable: | ||
is_a: CompoundExpression | ||
attributes: | ||
equipment: | ||
range: Equipment | ||
description: Name of the equipment used to measure a variable. | ||
variable: | ||
range: Variable | ||
description: Name of the variable being measured. | ||
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from __future__ import annotations | ||
from datetime import ( | ||
datetime, | ||
date, | ||
time | ||
) | ||
from decimal import Decimal | ||
from enum import Enum | ||
import re | ||
import sys | ||
from typing import ( | ||
Any, | ||
ClassVar, | ||
List, | ||
Literal, | ||
Dict, | ||
Optional, | ||
Union | ||
) | ||
from pydantic import ( | ||
BaseModel, | ||
ConfigDict, | ||
Field, | ||
RootModel, | ||
field_validator | ||
) | ||
metamodel_version = "None" | ||
version = "None" | ||
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class ConfiguredBaseModel(BaseModel): | ||
model_config = ConfigDict( | ||
validate_assignment = True, | ||
validate_default = True, | ||
extra = "forbid", | ||
arbitrary_types_allowed = True, | ||
use_enum_values = True, | ||
strict = False, | ||
) | ||
pass | ||
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class LinkMLMeta(RootModel): | ||
root: Dict[str, Any] = {} | ||
model_config = ConfigDict(frozen=True) | ||
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def __getattr__(self, key:str): | ||
return getattr(self.root, key) | ||
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def __getitem__(self, key:str): | ||
return self.root[key] | ||
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def __setitem__(self, key:str, value): | ||
self.root[key] = value | ||
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def __contains__(self, key:str) -> bool: | ||
return key in self.root | ||
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linkml_meta = LinkMLMeta({'default_prefix': 'ecosim_simple', | ||
'default_range': 'string', | ||
'description': 'Simple EcoSIM Extraction Template', | ||
'id': 'http://w3id.org/ontogpt/ecosim_simple', | ||
'imports': ['linkml:types', 'core'], | ||
'license': 'https://creativecommons.org/publicdomain/zero/1.0/', | ||
'name': 'ecosim_simple', | ||
'prefixes': {'ecosim': {'prefix_prefix': 'ecosim', | ||
'prefix_reference': 'http://purl.obolibrary.org/obo/ecosim'}, | ||
'ecosim_simple': {'prefix_prefix': 'ecosim_simple', | ||
'prefix_reference': 'http://w3id.org/ontogpt/ecosim_simple'}, | ||
'linkml': {'prefix_prefix': 'linkml', | ||
'prefix_reference': 'https://w3id.org/linkml/'}, | ||
'rdf': {'prefix_prefix': 'rdf', | ||
'prefix_reference': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'}}, | ||
'source_file': '/home/harry/ontogpt/src/ontogpt/templates/ecosim_simple.yaml', | ||
'title': 'Simple EcoSIM Extraction Template'} ) | ||
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class NullDataOptions(str, Enum): | ||
UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" | ||
NOT_APPLICABLE = "NOT_APPLICABLE" | ||
NOT_MENTIONED = "NOT_MENTIONED" | ||
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class ExtractionResult(ConfiguredBaseModel): | ||
""" | ||
A result of extracting knowledge on text | ||
""" | ||
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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input_id: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_id', 'domain_of': ['ExtractionResult']} }) | ||
input_title: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_title', 'domain_of': ['ExtractionResult']} }) | ||
input_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_text', 'domain_of': ['ExtractionResult']} }) | ||
raw_completion_output: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'raw_completion_output', 'domain_of': ['ExtractionResult']} }) | ||
prompt: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'prompt', 'domain_of': ['ExtractionResult']} }) | ||
extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""", json_schema_extra = { "linkml_meta": {'alias': 'extracted_object', 'domain_of': ['ExtractionResult']} }) | ||
named_entities: Optional[List[Any]] = Field(None, description="""Named entities extracted from the text""", json_schema_extra = { "linkml_meta": {'alias': 'named_entities', 'domain_of': ['ExtractionResult']} }) | ||
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class NamedEntity(ConfiguredBaseModel): | ||
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', | ||
'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, | ||
'comments': ['this is populated during the grounding and normalization step'], | ||
'domain_of': ['NamedEntity', 'Publication']} }) | ||
label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', | ||
'aliases': ['name'], | ||
'annotations': {'owl': {'tag': 'owl', | ||
'value': 'AnnotationProperty, AnnotationAssertion'}}, | ||
'domain_of': ['NamedEntity'], | ||
'slot_uri': 'rdfs:label'} }) | ||
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class CompoundExpression(ConfiguredBaseModel): | ||
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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pass | ||
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class Triple(CompoundExpression): | ||
""" | ||
Abstract parent for Relation Extraction tasks | ||
""" | ||
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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subject: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'subject', 'domain_of': ['Triple']} }) | ||
predicate: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'predicate', 'domain_of': ['Triple']} }) | ||
object: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object', 'domain_of': ['Triple']} }) | ||
qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""", json_schema_extra = { "linkml_meta": {'alias': 'qualifier', 'domain_of': ['Triple']} }) | ||
subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""", json_schema_extra = { "linkml_meta": {'alias': 'subject_qualifier', 'domain_of': ['Triple']} }) | ||
object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""", json_schema_extra = { "linkml_meta": {'alias': 'object_qualifier', 'domain_of': ['Triple']} }) | ||
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class TextWithTriples(ConfiguredBaseModel): | ||
""" | ||
A text containing one or more relations of the Triple type. | ||
""" | ||
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication', | ||
'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, | ||
'domain_of': ['TextWithTriples', 'TextWithEntity']} }) | ||
triples: Optional[List[Triple]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'triples', 'domain_of': ['TextWithTriples']} }) | ||
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class TextWithEntity(ConfiguredBaseModel): | ||
""" | ||
A text containing one or more instances of a single type of entity. | ||
""" | ||
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication', | ||
'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, | ||
'domain_of': ['TextWithTriples', 'TextWithEntity']} }) | ||
entities: Optional[List[str]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'entities', 'domain_of': ['TextWithEntity']} }) | ||
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class RelationshipType(NamedEntity): | ||
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core', | ||
'id_prefixes': ['RO', 'biolink']}) | ||
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id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', | ||
'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, | ||
'comments': ['this is populated during the grounding and normalization step'], | ||
'domain_of': ['NamedEntity', 'Publication']} }) | ||
label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', | ||
'aliases': ['name'], | ||
'annotations': {'owl': {'tag': 'owl', | ||
'value': 'AnnotationProperty, AnnotationAssertion'}}, | ||
'domain_of': ['NamedEntity'], | ||
'slot_uri': 'rdfs:label'} }) | ||
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class Publication(ConfiguredBaseModel): | ||
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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id: Optional[str] = Field(None, description="""The publication identifier""", json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['NamedEntity', 'Publication']} }) | ||
title: Optional[str] = Field(None, description="""The title of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'title', 'domain_of': ['Publication']} }) | ||
abstract: Optional[str] = Field(None, description="""The abstract of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'abstract', 'domain_of': ['Publication']} }) | ||
combined_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'combined_text', 'domain_of': ['Publication']} }) | ||
full_text: Optional[str] = Field(None, description="""The full text of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'full_text', 'domain_of': ['Publication']} }) | ||
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class AnnotatorResult(ConfiguredBaseModel): | ||
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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subject_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'subject_text', 'domain_of': ['AnnotatorResult']} }) | ||
object_id: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object_id', 'domain_of': ['AnnotatorResult']} }) | ||
object_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object_text', 'domain_of': ['AnnotatorResult']} }) | ||
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class TermSet(NamedEntity): | ||
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/ecosim_simple', 'tree_root': True}) | ||
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terms: Optional[List[str]] = Field(None, description="""A semicolon-separated list of variables for earth system simulation. Do not include abbreviations in parentheses, e.g., \"Carbon (C)\" should be represented as \"carbon\". Examples include: carboxylation, sodium, underground irrigation.""", json_schema_extra = { "linkml_meta": {'alias': 'terms', 'domain_of': ['TermSet']} }) | ||
id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', | ||
'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, | ||
'comments': ['this is populated during the grounding and normalization step'], | ||
'domain_of': ['NamedEntity', 'Publication']} }) | ||
label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', | ||
'aliases': ['name'], | ||
'annotations': {'owl': {'tag': 'owl', | ||
'value': 'AnnotationProperty, AnnotationAssertion'}}, | ||
'domain_of': ['NamedEntity'], | ||
'slot_uri': 'rdfs:label'} }) | ||
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class Term(NamedEntity): | ||
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'annotators': {'tag': 'annotators', | ||
'value': 'bioportal:ECOSIM'}, | ||
'prompt': {'tag': 'prompt', | ||
'value': 'The name of a variable for earth system ' | ||
'simulation.'}}, | ||
'from_schema': 'http://w3id.org/ontogpt/ecosim_simple'}) | ||
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id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', | ||
'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, | ||
'comments': ['this is populated during the grounding and normalization step'], | ||
'domain_of': ['NamedEntity', 'Publication']} }) | ||
label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', | ||
'aliases': ['name'], | ||
'annotations': {'owl': {'tag': 'owl', | ||
'value': 'AnnotationProperty, AnnotationAssertion'}}, | ||
'domain_of': ['NamedEntity'], | ||
'slot_uri': 'rdfs:label'} }) | ||
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# Model rebuild | ||
# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model | ||
ExtractionResult.model_rebuild() | ||
NamedEntity.model_rebuild() | ||
CompoundExpression.model_rebuild() | ||
Triple.model_rebuild() | ||
TextWithTriples.model_rebuild() | ||
TextWithEntity.model_rebuild() | ||
RelationshipType.model_rebuild() | ||
Publication.model_rebuild() | ||
AnnotatorResult.model_rebuild() | ||
TermSet.model_rebuild() | ||
Term.model_rebuild() |
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,39 @@ | ||
id: http://w3id.org/ontogpt/ecosim_simple | ||
name: ecosim_simple | ||
title: Simple EcoSIM Extraction Template | ||
description: >- | ||
Simple EcoSIM Extraction Template | ||
license: https://creativecommons.org/publicdomain/zero/1.0/ | ||
prefixes: | ||
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# | ||
linkml: https://w3id.org/linkml/ | ||
ecosim_simple: http://w3id.org/ontogpt/ecosim_simple | ||
ecosim: http://purl.obolibrary.org/obo/ecosim | ||
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default_prefix: ecosim_simple | ||
default_range: string | ||
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imports: | ||
- linkml:types | ||
- core | ||
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classes: | ||
TermSet: | ||
tree_root: true | ||
is_a: NamedEntity | ||
attributes: | ||
terms: | ||
range: Term | ||
multivalued: true | ||
description: >- | ||
A semicolon-separated list of variables | ||
for earth system simulation. Do not include | ||
abbreviations in parentheses, e.g., "Carbon (C)" | ||
should be represented as "carbon". Examples include: carboxylation, sodium, underground irrigation. | ||
Term: | ||
is_a: NamedEntity | ||
annotations: | ||
annotators: bioportal:ECOSIM | ||
prompt: >- | ||
The name of a variable for earth system simulation. |
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